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Prokaryotes III - Evolution and Early Metabolism

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Introduction and Goals

The last two tutorials discussed the diversity of prokaryotes, their structure, and their diverse metabolisms. Prokaryotes can use a variety of nitrogen and carbon sources, and in doing so they are important members of the biosphere. Prokaryotes also are involved in important relationships with many other types of organisms. After working through this tutorial you should understand:

  • How bacteria can be beneficial
  • Symbiotic relationships between prokaryotes and other life forms
  • Nitrogen use and the prokaryote
  • Oxygen and metabolic relationships
  • Origins of metabolic processes

Performance Objectives:

  • Categorize the different types of relationships seen among organisms and be able to cite examples of each type in the bacteria
  • Describe the impact of prokaryotes on the environment of the early Earth

The Social Life of Prokaryotes

From some of the examples in the previous tutorials, you might have concluded that most bacteria are pathogens that cause diseases. However, this generalization would be wrong. In fact, the vast majority of bacteria around us are either essential or harmless to the life of other organisms (including ourselves). Humans are covered with bacteria (both inside and out). You may find this fact unsettling, but right now there are approximately 400 different species of bacteria living in your gastrointestinal system.

Only a relatively small percentage of the bacterial species that colonize us (and all other multicellular organisms) are pathogenic. The vast majority of bacteria are ecologically significant and extremely beneficial. In most instances, bacteria colonize on and live harmlessly with other species.

The state of any two species having an extended and intimate association is termed symbiosis. You might have heard other definitions for this term, but researchers in the field agree that this is the best definition.


Types of Symbioses

The interacting organisms (symbionts) have varying relationships with one another. The host (the larger of two species) and the microsymbiont (the smaller of the two species) may derive mutual benefit from the association, in which case the symbiosis is termed mutualism. At the other end of the symbiotic spectrum is a relationship whereby one member of the symbiosis derives benefit at the expense of the other, which is termed parasitism. In the middle of this spectrum are associations which appear benign (are neither of benefit nor harm) to either or both species; this form of symbiosis is termed commensalism. These are not fixed relationships, and the association between the symbionts is not constant and can change, depending on conditions. For example, a relationship may be commensalistic (or even mutualistic) most of the time, but under certain conditions the association can turn parasitic.


Symbiosis is not a static process. Commensalistic or mutualistic relationships can quickly degrade into parasitic relationships depending on environmental conditions. For instance, the bacteria in your intestines play an important role in processing food into absorbable nutrients. This symbiotic relationship is mutualistic, but a punctured intestine can release the bacteria into other parts of the body where they can quickly induce sepsis, an often fatal condition. This sort of event is known as an opportunistic infection, where a normally commensalistic bacteria becomes pathogenic in response to a changed environment (usually a weakened immune system). Penn State’s Center for Sports Surface Research has examined the role of synthetic turf in staph infections (Figure 1 -

Figure 1.  Synthetic turf and staph infections

Why is this a concern?  Did their study provide evidence that synthetic turf increases the risk of staph infections in athletes?  Was there a difference between the survival of staph on outdoor versus indoor synthetic turf? 


Mutualistic Symbioses

Quite a few mutualistic symbioses involving prokaryotes are known, but unfortunately they don't get nearly the attention they deserve. Without their existence, however, life as we know it would not exist. Let's consider a few examples.

Nitrogen is essential to all life. It is required for the synthesis of nucleic acids, proteins, and a host of other important biomolecules. However, without the action of certain prokaryotes, little nitrogen would be available to the biosphere. There are several species of bacteria that can convert atmospheric nitrogen (N2) into a form (e.g., ammonium) that can be used by other life. One of the most important groups are those bacteria that form a symbiosis with certain plants. For example, Rhizobium bacteria colonize on the roots of pea plants, where they fix nitrogen. The plant provides carbon to the bacteria, and the bacteria provide nitrogen to the plant; a classic and extremely important example of a mutualistic symbiosis. We will discuss this further in the section on the Nitrogen Cycle below.

Humans serve as a host for a number of mutualistic symbioses with prokaryotes. Researchers have studied these to varying degrees. For example, one (or more) of the bacteria species that colonize our lower gastrointestinal tract has the ability to synthesize vitamin K (which humans cannot produce). Vitamin K is taken up by your intestines and used in blood-clotting (and possibly other reactions). In this symbiosis, humans get an essential vitamin and the bacteria get a source of carbon from the food we do not completely digest. (The majority of bacteria in our GI tract are located past the major nutritive absorbing areas of the intestine.)

The mutualistic symbioses between prokaryotes and humans may also play a more general and important role. Studies in mice have shown that mice raised in very clean facilities that did not acquire gut bacteria are much more likely to develop Type 1 diabetes than mice raised in “dirty” facilities, where bacteria were present.  Go to this article that discusses the role of germ exposure during early infant development, and take notes on the role that symbiotic bacteria may play in the development of specific cells involved in the human immune system.



In a parasitic symbiosis, one member of the symbiosis benefits at the expense of another. Parasitic bacteria that cause disease in their hosts are called pathogens. These pathogenic bacteria cause disease by either invading healthy host tissue or by producing toxins that poison the host. Exotoxins are proteins secreted by prokaryotes, whereas endotoxins are surface protein components of the outer cell membrane in some gram-negative bacteria. Clostridium botulinum (the causative agent of botulism) is a notorious exotoxin-secretor, as is Vibrio cholerae, which causes cholera. The causative agent of typhoid fever, Salmonella typhi, produces endotoxins that counteract the human host's natural defenses.

Figure 2.  Clostridium botulinum, from CDC

Cholera and the Importance of Water Balance

Vibrio cholerae is spread via contaminated water supplies, and people who drink water tainted with this organism can succumb to cholera. The mortality rate of untreated, symptomatic individuals can be quite high; afflicted individuals can die within 24 hours if not treated promptly. The bacteria itself does not cause the disease, rather it is the exotoxin it secretes.

To understand how cholera kills, you need to know about osmosis (the net movement of water across a selectively permeable membrane, from lower solute concentrations to higher solute concentrations). So, what does osmosis have to do with cholera? Everything.

Vibrio cholera colonizes the intestines. The exotoxin (cholera toxin) stimulates the cells that line the lower GI tract (the intestinal epithelium) to secrete massive amounts of excessive ions into the lumen (the cavity) of the intestine. This creates an extremely hypertonic state within the intestinal lumen, relative to the epithelium. Think about the consequences of this in terms of osmosis, and be prepared to make a prediction regarding the most severe symptoms of cholera.


Figure 3.  Effect of adding L-histidine to an ORS on the output of diarrhea in individuals infected with cholera (Click to enlarge) (

Cholera and other diarrheal diseases are the number two cause of infant mortality worldwide, and collectively kill more than 2 million people annually. Most of these deaths are entirely preventable with inexpensive rehydration therapy using an oral rehydration solution (ORS).  Looking at Figure 3, what effect, if any, does the addition of the amino acid L-histidine to an ORS have on the treatment of cholera?  Is the duration of the treatment important?

The Body As a Community

Remember that our own bodies are teeming with bacteria, as are virtually all eukaryotes. At birth we were devoid of bacteria, but as we acquired bacteria through feeding, and simply by being around other humans and the environment, our bodies became colonized with hundreds of different species of bacteria. The relative proportions of these species are variable. However, some of our commensalistic bacteria can become parasitic when our natural defense mechanisms become depressed.


In Summer 2012, research groups published major findings from the Human Microbiome Project; the genetic material of bacteria taken from 242 healthy people was sequenced by a team of 200 scientists from 80 different institutions.  They found that each person had about 1000 different strains of bacteria living on or in their bodies (two to five pounds!), and that this “microbiome” was different for each person. All individuals had some disease-causing bacteria in their microbiome, but it was not causing disease. They also discovered that babies born via a C-section had different microbiomes than babies born vaginally. As a scientist, what would you do to follow up on this finding?

Figure 4.  Human Microbiome Project Image from the NIH.

The relationship between host and symbiont can be quite complex. Termites are a good example of this complexity. We normally think of these insects as wood eaters, and indeed they can dine on our homes. However, they themselves cannot directly digest the wood. Inside the termite gut is a menagerie of protists (to be discussed in future tutorials) that ingest the wood particles consumed by the termite. But even these protists cannot directly digest the cellulose. Rather, living in and around the protozoa are bacteria that can degrade the wood. So it is the microsymbiont living within the microsymbiont of the termite host that actually degrades the wood. Life is interrelated in surprising ways.


The Global Impact of Prokaryotes and the Nitrogen Cycle

Nitrogen is found in all proteins and nucleic acids, hence it is essential to all forms of life. This atom is abundant in the air around us in the form of atmospheric nitrogen. However, nitrogen availability is a problem because nitrogen, in its elemental form (N2 gas), is not usable by most organisms. Nitrogen can only be transformed into a biologically usable state (i.e., "fixed") by certain nitrogen-fixing bacteria, in a process termed nitrogen fixation. "Nitrogen-fixers" live in the aquatic environment, the soil, and in or around the roots and stems of certain species of plants.

Nitrogen gas (also known as dinitrogen or N2) is converted to ammonia (NH3) by nitrogen-fixing bacteria. The fixed nitrogen is then used by plants (and other soil- and aquatic-dwelling microorganisms) in various anabolic pathways leading to the synthesis of proteins, nucleic acids, and other nitrogenous molecules.


Plants, the primary energy producers in the terrestrial environment, are a major repository for fixed nitrogen in the terrestrial biosphere. When a plant is eaten, the herbivore obtains nitrogen in the form of proteins and nucleic acids (which are broken down during digestion and used by the herbivore for the production of its own nitrogen products). When a plant dies, a variety of saprobes (those organisms that live on dead and decaying matter) also obtain nitrogen from the nitrogenous compounds previously made by the plant. Finally, fixed nitrogen can be reconverted by soil bacteria back into atmospheric nitrogen. The nitrogen cycle (Figure 5) is essential for all life on the planet. The previous tutorial briefly introduced the symbiosis that leads to nitrogen fixation. We will now examine this symbiosis in more detail.

Figure 5.  Overview of Nitrogen Fixation. (Click to enlarge)


The Nitrogen Fixers

Figure 6.  Root Nodules of a Soybean Plant.

Bacteria, housed in these root nodules, fix nitrogen for this soybean plant.

Figure 7. A Rhizobium.

Almost all legumes (e.g., peas, alfalfa, and soybeans) are capable of housing nitrogen-fixing bacteria. The plant-prokaryote mutualism (the plant gets fixed nitrogen from the bacteria, while the bacteria get carbon from the plant) that results is determined by a complex series of events that begins with chemical communication between the participating organisms. Plants that participate in these symbioses secrete molecules (e.g., flavonoids) that act as chemical signals to a select species of bacteria. The term rhizobia is applied to several species of bacteria that participate in these symbioses. The targeted rhizobia are induced to respond when the specific chemical signal stimulates specific genes to "turn on." Bacteria then migrate toward the plant's root. Once bacteria reach the root, a developmental change is induced in the root, which results in nodule formation (Figure 6). The Rhizobium bacteria (Figure 7) take up residence inside the nodule. Thus, the events of nodule formation involve chemical cross-signaling between the two participants. The environment of the plant-derived nodule is favorable for the fixation of nitrogen by the bacteria that live inside.


In addition to rhizobia/legume symbioses, several other symbiotic nitrogen-fixing symbioses are known. For example, various species of Cyanobacteria (often referred to as blue-green algae – Figure 8) are capable of nitrogen fixation. One symbiosis is particularly important to humanity. Anabaena is a Cyanobacterium genus that colonizes on the leaves of an aquatic fern that grows in rice paddies; the symbiosis supplies nitrogen to the pond, where it subsequently is taken up and used by rice plants. About 75% of all rice is cultivated in flooded fields, and this symbiosis has allowed rice farmers to maintain high levels of productivity without the need for expensive chemical fertilizers.

Figure 8.  A Cyanobacterium. (Click to enlarge)

The Global Impact of Prokaryotes and Oxygen

It may be hard to envision life without oxygen, but the first prokaryotes (the first organisms on Earth) evolved in an environment with essentially no molecular oxygen (oxygen gas, or O2). Consequently, the first prokaryotes, which originated between 3.5 and 4 billion years ago, were anaerobic. Anaerobic is a general term that refers to any organism, environment, or cellular process that lacks or does not require oxygen, and can even be poisoned by oxygen.

The original anaerobic organisms thrived in an environment devoid of oxygen. Many scientists think that the early prokaryotes were chemoautotrophs, obtaining energy from inorganic chemicals, possibly using the then-abundant hydrogen sulfide (H2S). Evidence to support this hypothesis can be observed in some hot springs, which contain members of the Archaea. They obtain energy from the combining of ferrous sulfide (FeS) and hydrogen sulfide (H2S) in a redox reaction, which releases energy.

  • FeS + H2S → FeS2 + H2

The cyanobacteria, originating between 2.5 and 3.4 billion years ago, were the first photosynthetic bacteria to use water (H2O) as an electron source. They released oxygen as a waste product. These photosynthetic organisms thrived wherever there was sufficient light and a body of water. However, this created a problem on a global scale. After several hundred million years, free oxygen began to accumulate in the atmosphere, which marks the change from a reducing to an oxidizing atmosphere.  Evidence for this great oxygenation event (Figure 9) can be seen in the geological record.  Initially the high levels of free oxygen were toxic to life. Organisms underwent adaptation through several mechanisms that mitigate this problem, including the use of oxygen in metabolism. Because we need oxygen for our survival, it is hard to believe that oxygen is toxic to many life forms.


Figure 9.  The timing of the Great Oxygenation Event based upon biological and geological information (

Today prokaryotes (and other life forms) exhibit various metabolic relationships with oxygen. Obligate aerobes require oxygen, whereas obligate anaerobes have no need for oxygen and may even be poisoned by oxygen. Facultative anaerobes can alternate their oxygen requirement. They can use oxygen if it is present, but they can also function in an anaerobic environment. In the upcoming tutorials on energy and cellular respiration, the role of oxygen in cellular processes and how anaerobic organisms get by without oxygen will be addressed.



A great deal of life on the planet depends on prokaryotes, either directly or indirectly. Many prokaryotes form intimate associations with other species. These symbiotic relationships can take on a variety of forms. At one extreme are the mutualistic relationships. In a mutualistic symbiosis, both species derive benefit from the association; the bacteria that live in our lower digestive tract provide us with a number of vitamins and, in turn, we provide them with a source of carbon from the food we do not digest ourselves. At the other extreme is a parasitic symbiosis, in which the symbiont benefits at the expense of the host. Such parasitic bacteria are usually termed pathogenic because they can cause serious diseases. Microbiologists have provided us with an appreciation for prokaryotes, and their discoveries have led to new opportunities for using prokaryotes to better humanity and to combat diseases caused by pathogenic bacteria.

Prokaryotes are an important component of ecosystems. The saprophytes degrade material from dead organic matter, and in doing so make nitrogen and carbon available to other life forms. Without them, nutrients would quickly be tied up in the carcasses of dead organisms and unavailable for other organisms in the ecosystem.

Nitrogen is necessary for the synthesis of amino acids. As with carbon, bacteria obtain their nitrogen from various sources. Some bacteria can convert ammonia into a more useful form of nitrogen (like nitrates and nitrites). Saprophytic bacteria obtain their nitrogen from decaying organic matter, whereas nitrogen-fixing bacteria obtain their nitrogen from molecular nitrogen (N2) found in the atmosphere.

Cyanobacteria not only fix their own nitrogen from the air, but they also synthesize their own sugars from carbon dioxide, using sunlight as an energy source. They may be the most efficient form of life on the planet. Indeed, the ancestors of blue-green algae played an important role in the history of the planet because their photosynthetic activity converted our planet's early anaerobic environment into one that is oxygen rich.

We also examined the relationships between oxygen and metabolism, and  later in the course we will explore, in more detail, the relationship between energy and metabolic processes.



After reading this tutorial, you should have a working knowledge of the following terms:

  • anaerobic
  • antibiotic
  • commensalism
  • Cyanobacteria
  • endotoxin
  • exotoxin
  • facultative anaerobe
  • host
  • legume
  • microbiome
  • microsymbiont
  • mutualism
  • nitrogen cycle
  • nitrogen fixation
  • nodule
  • obligate aerobe
  • obligate anaerobe
  • opportunistic infection
  • osmosis
  • parasitism
  • rhizobia
  • saprobe
  • symbiont
  • symbiosis

Case Study for Prokaryotes III

The adult human intestine is home to up to 100 trillion bacteria (this is 10x the number of cells that make up an adult human).  It has been suggested that the human intestine achieves the highest cell densities of any ecosystem on earth. 

 Recently we have discovered that the presence of these bacteria gives us metabolic capacities that we have not evolved for ourselves.  For example, Bacteroides thetaiotaomicron is very good at digesting polysaccharides that we find indigestible.  By breaking down these polysaccharides, they produce smaller compounds that our bodies can use for nutrients and energy.

 When Bacteroides thetaiotaomicron escapes the gut, it can cause infections and abscesses in many parts of the body.  Infection from Bacteroides thetaiotaomicron is an important side effect of abdominal surgeries and populations of the bacteria are almost universally resistant to penicillin.

 Our symbiotic relationship with many of these gut bacteria has traditionally been referred to as commensalism.  Our recent findings, however, suggest this is not correct and we need to update our understanding of our symbiotic relationships with our gut bacteria, including Bacteroides thetaiotaomicron.

Cross section of a Bacteroides showing an outer membrane with attached lipopolysaccharides, a thin peptidoglycan layer, and a cytoplasmic membrane.

  • Briefly explain why commensalism is not an adequate description of our relationship with Bacteroides thetaiotaomicron.
  • What is our symbiotic relationship with Bacteroides thetaiotaomicron?
  • Is Bacteroides thetaiotaomicrona a gram negative or gram positive bacterium?

Now that you have read this tutorial and worked through the case study, go to ANGEL and take the tutorial quiz to test your understanding.  Questions?  Either send your instructor a message through ANGEL or attend instructor office hours (the times and places are posted on ANGEL).